HLA-DP diversity is associated with improved response to SARS-Cov-2 vaccine in hematopoietic stem cell transplant recipients

Summary Allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients show lower humoral vaccine responsiveness than immunocompetent individuals. HLA diversity, measured by the HLA evolutionary divergence (HED) metrics, reflects the diversity of the antigenic repertoire presented to T cells, and has been shown to predict response to cancer immunotherapy. We retrospectively investigated the association of HED with humoral response to SARS-CoV-2 vaccine in allo-HSCT recipients. HED was calculated as pairwise genetic distance between alleles at HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1 loci in recipients and their donors. Low anti-spike IgG levels (<30 BAU/mL) were associated with short time from allo-SCT and low donor DPB1-HED, mostly related to donor DPB1 homozygosity. The diversity of donor HLA-DP molecules, assessed by heterozygosity or sequence divergence, may thus impact the efficacy of donor-derived CD4 T cells to sustain vaccine-mediated antibody response in allo-HSCT recipients.


INTRODUCTION
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients show dampened immune responses to SARS-CoV-2 vaccine, 1 despite the immunogenicity of this vaccine in the general population. Presentation of vaccine antigens to T lymphocytes is an essential component of vaccine immune response. The highly polymorphic HLA class I (HLA-A, -B, and-C) and class II (HLA-DR, -DQ, and -DP) molecules bind and present vaccine-derived peptides, to CD8 and CD4 T lymphocytes respectively, subsequently initiating antigen-specific immune responses. According to the heterozygote advantage, originally observed in the context of infectious diseases, heterozygous HLA genotypes enable presentation of a wider repertoire of antigenic peptides to T cells, which in turn supports a more diversified T cell response. 2,3 The functional difference between two HLA alleles can be further captured by the HLA evolutionary divergence (HED) metric, which quantifies the sequence divergence between the peptide-binding domains of two homologous alleles at a given locus and provides a primary measure of the breadth of the immunopeptidome presented to T cells. We and others have shown that HED is associated with the strength of T cell responses in various clinical contexts, such as response to cancer immunotherapy, autoimmunity, and allogeneic responses. [4][5][6][7][8][9] Herein, we report the impact of HLA diversity on humoral response to SARS-CoV-2 vaccine in allo-HSCT recipients.

RESULTS
We studied 156 adult allo-HSCT recipients who received two doses of the Pfizer BNT162b2 vaccine 3 to 4 weeks apart between January and July 2021 at a median time of 44 months (range 3-205) after transplantation. Clinical and biological characteristics of the patients are shown in Table 1. No patient was vaccinated earlier than 3 months post-HSCT and none had a clinical history of COVID-19. At the time of vaccination, 71 (45.5%) patients still received graft versus host disease (GVHD) prophylactic or immunosuppressive treatment. Anti-SARS-CoV-2 Spike protein (S) IgG was routinely quantified as binding antibody units (BAU/mL) 30 days after the second dose. Serology at baseline was not available in all patients and was therefore not considered. According to guidances from the Francophone Society of Bone Marrow Transplantation and Cellular Therapy (SFGM-TC), non-responders were defined as anti-S IgG levels <30 BAU/mL, low responders as < 30 but <250 BAU/mL, and strong responders as R 250 HLA-A, -B, -C, -DRB1, -DQB1, and -DPB1 typing at second field resolution was previously performed in all recipients and their donors. The protein sequence divergence (HED) was calculated for all allele pairs at each locus in both recipients and donors.
In univariate analysis comparing responders to nonresponders, shorter time from allo-HSCT and homozygosity or low HED at the DPB1 locus of the donor were associated with no response (Table 1). Donor DPB1 homozygosity was more frequent in nonresponders than in responders (50% versus 20.3%, p = 0.012). Of the 37 recipients of DPB1* homozygous donors, 9 were nonresponders compared to only 9 of the 117 recipients of DPB1* heterozygous donors (24% and 7.7%, respectively, p = 0.005). Moreover, DPB1-HED was lower in nonresponders than in responders (mean 4.0 versus 1.4, p = 0.023), with no significant difference between low and strong responders (Figure 1). We observed no effect of recipient homozygosity or HED at any locus, or of donor-recipient HLA mismatch, specifically DPB1 mismatch (Table 1). No individual HLA allele of the donor or the recipient was associated with the vaccine response. In particular, the genome-wide significant association of HLA-DQB1*06 alleles with higher levels of antispike IgG at 28 days after the first dose of the ChAdOx1 nCoV-19 vaccine in participants of a large vaccine efficacy trial in the United Kingdom 10 was not observed in our smallest allo-HSCT cohort (DQB1*06 present in 34.7% of responders and 38.8% of nonresponders, ns). Moreover, the frequency of DPB1*04:01, which is among the most common HLA alleles in the general population and could have explained the effect of DPB1 homozygosity or HED, was equally distributed in responders and nonresponders (65.2% and 66.6%, respectively) ( Table 1). Notably, the response rate did not differ by donor type (haplo-identical, mismatched unrelated, or fully matched unrelated or related), immunosuppression status (ongoing treatment with steroids, ruxolitinib, or cyclosporine), presence of active acute or chronic GVHD, or immunological recovery (total, CD8 and CD4 T, B and NK lymphocyte counts) at the time of vaccination (Table 1).
In multivariate logistic analysis, lack of vaccine response was associated with shorter time from allo-SCT (p = 0.033), donor DPB1 homozygosity (p = 0.031) or low donor DPB1-HED (p = 0.010). When excluding the 37 DPB1 homozygous donors, the significant effect of DPB1-HED was lost, suggesting that the lower response rate was mainly related to DPB1 homozygosity.

DISCUSSION
The development of anti-SARS-CoV-2 immunity is particularly important in allo-SCT recipients, as they have poor outcome after COVID-19 infection. We found that 88.5% of allo-SCT recipients developed an anti-S IgG response after 2 doses of the BNT162b2, a high rate in line with other studies with this vaccine. 11,12 SARS-CoV-2 mRNA vaccines have a strong ability to induce CD4 follicular helper T (T FH ) cell responses which support germinal center formation and differentiation of memory and antibody-secreting B cells. 13,14 Therefore, it is not surprising that the diversity of donor HLA class II molecules, assessed by heterozygosity or sequence divergence, may impact the efficacy of donor-derived CD4 T cells to sustain vaccine-mediated antibody response in allo-HSCT recipients. As expected, with the progressive replacement of the recipient's immune system by a new one derived from donor HSCs, no effect of the recipient's HLA diversity was observed in our study. Interestingly, the predominant role of HLA-DPB1 relative to -DRB1 and -DQB1 is fully consistent with a recent study highlighting the key role of DPB1-restricted T FH responses iScience Article against immunodominant spike peptides in establishing a robust and persistent immunity after BNT162b2 vaccine in healthy individuals. 14 Moreover, recent data point to unique features of HLA-DP molecules that can bind peptides in a reverse orientation, thereby broadening the antigen repertoire recognized by CD4 T cells. 15 Limitations of the study Our study is limited by the relatively small sample size of our cohort, lack of baseline serology in most patients, and antibody titers measured with three different commercial assays. However, it helps in understanding mechanisms of impaired vaccine immune response in immunosuppressed patients. Notably, the 18 nonresponders received a third vaccine dose, of whom 16 had serological evaluation: 4 still failed to mount a serological response and 3 of them (75%) had a DPB1 homozygous donor, compared to 5 of the 12 responders (41.7%). If confirmed in a replication cohort, these data suggest that allo-HSCT recipients of DPB1 homozygous donors should be offered a different platform for a subsequent vaccination.

STAR+METHODS
Detailed methods are provided in the online version of this paper and include the following: